Can I directly write checks from my IRA to a qualified charitable organization or do I have to have the custodian/trustee write them?

No.  "A QCD is generally a nontaxable distribution made directly by the trustee of your IRA (other than a SEP or SIMPLE IRA) to an organization eligible to receive tax-deductible contributions. You must be at least age 701/2 when the distribution was made. Also, you must have the same type of acknowledgment of your contribution that you would need to claim a deduction for a charitable contribution."

Please see IRS Pub. 590-B: Distributions from Individual Retirement Arrangements (IRAs) ( (page 13)